For decades, the story of how humans first populated South America was told in two chapters: an initial wave of migration around 12,000 years ago, and a second one roughly 9,000 years ago.
However, a new study has found a third chapter that nobody had documented before.
The research was coordinated by Tábita Hünemeier, a geneticist at the University of São Paulo’s Institute of Biosciences.
The team fully sequenced 128 genomes and compared them with 71 previously published sequences, covering 45 Indigenous groups across eight Latin American countries: Argentina, Bolivia, Brazil, Colombia, Ecuador, Mexico, Paraguay, and Peru.
What the data revealed was that a significant proportion of the ancestry of today’s Indigenous South Americans traces back to a migration from Mesoamerica – what is now Mexico – that happened around 1,300 years ago.
This third wave had never been identified before. It is now known to be the one most represented in the current population.
Three waves instead of two
The first wave of migration into South America left its clearest traces in places like the Lapa do Santo site and Sumidouro cave in the Lagoa Santa region of Brazil, as well as in Chile, with records going back up to 12,000 years.
Around 9,000 years ago, a second wave arrived, leaving distinct marks in both the genetic and archaeological records in Peru and Argentina.
Between these two waves and the arrival of the third, the Middle Holocene period brought significant environmental disruption roughly 8,000 to 4,200 years ago.
This led to degraded ecosystems and reduced resources, putting pressure on human populations across the continent.
Then, around 1,300 years ago, came the migration from Mesoamerica. The people who arrived in this third wave became, over subsequent centuries, the primary genetic ancestors of many of today’s Indigenous South Americans.
That this wave went undetected for so long reflects both the limits of previous genomic tools and the lack of comprehensive genetic data from the Americas.
What happened after European contact
The study also traced what happened after Europeans arrived in the 16th century. The genetic data tells a grim story that aligns with the historical record.
Indigenous groups became less numerous and more genetically isolated from one another after contact.
This pattern is consistent with population collapse driven by epidemic disease, enslavement, and the systematic destruction of subsistence practices and traditional knowledge.
The research detected clear signs of inbreeding – reproduction within very small, isolated groups with no possibility of migration or intermarriage – among the Sirionó, Suruí, and Karitiana peoples within the Tupi lineage.
This is a genetic signature of catastrophic population reduction, not of ancient cultural practice.
Some recovery is visible in the data, particularly in parts of western South America. Genetic diversity is higher in Central America and in the Southern Cone.
But the scars of the colonial period are written into the genomes of living people in ways that remain measurable centuries later.
Traces of different genomic segments
One of the study’s more puzzling findings involves ancient genomic segments found in South American DNA that shouldn’t, on a straightforward reading of migration history, be there.
The genomes of some Indigenous South Americans contain traces characteristic of Australasians, as well as of Neanderthals from Europe and Denisovans from East Asia.
The presence of these ancient genetic segments isn’t entirely new to science, but their persistence is.
The researchers’ hypothesis is that these sequences have been maintained by natural selection.
This means they confer some benefit, probably related to immune response, metabolic function, fertility, or other traits, even if that benefit hasn’t yet been identified.
The current study wasn’t designed to answer that functional question, but it flags it clearly as territory for future research.
Importance of Indigenous involvement
One detail about this research is worth noting separately. The study was conducted exclusively by researchers from Latin America.
Among the authors is Putira Sacuena, a biomedical scientist from the Federal University of Pará, whom Hünemeier describes as the first Indigenous woman to work in genetic anthropology.
The researchers consider the inclusion of Indigenous collaborators in studies about Indigenous peoples to be both ethically important and scientifically valuable.
Filling an important gap
The absence of comprehensive genomic data from the Americas has been a persistent problem for population genetics.
The markers used in many previous studies were designed based on European and African populations, making them poorly suited to characterizing the genetic diversity of the Americas.
André Strauss, an archaeologist at the University of São Paulo’s Museum of Archaeology and Ethnology, did not participate in the study but has published extensively on the ancient history of South American populations.
Strauss described the new findings as answering a question that his own 2018 research had left open.
His earlier work established that the people of Lagoa Santa – the ancient population whose remains have been found at sites like Lapa do Santo – were not the direct ancestors of today’s Indigenous South Americans. But if not them, then who?
“The current article confirms the two previous migratory waves and characterizes the third,” Strauss said.
Future research directions
Identifying that third wave in the archaeogenetic record – the physical bones and ancient DNA that would confirm the genomic picture – is now the next task.
This task is complicated by the fact that most available skeletal material predates the third migration, and that organic material decays rapidly in environments like the Amazon.
But the team already has more than a thousand additional sequenced samples in progress.
“We understand that to grasp the diversity and complexity of the Americas, it’s best to have a few individuals from many populations,” Hünemeier concluded.
The study is published in the journal Nature.